17 research outputs found
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Steric trapping reveals a cooperativity network in the intramembrane protease GlpG.
Membrane proteins are assembled through balanced interactions among proteins, lipids and water. Studying their folding while maintaining the native lipid environment is necessary but challenging. Here we present methods for analyzing key elements of membrane protein folding including thermodynamic stability, compactness of the unfolded state and folding cooperativity under native conditions. The methods are based on steric trapping, which couples the unfolding of a doubly biotinylated protein to the binding of monovalent streptavidin (mSA). We further advanced this technology for general application by developing versatile biotin probes possessing spectroscopic reporters that are sensitized by mSA binding or protein unfolding. By applying these methods to the Escherichia coli intramembrane protease GlpG, we elucidated a widely unraveled unfolded state, subglobal unfolding of the region encompassing the active site, and a network of cooperative and localized interactions to maintain stability. These findings provide crucial insights into the folding energy landscape of membrane proteins
Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography–Capillary Zone Electrophoresis–Tandem Mass Spectrometry
Native proteomics aims to characterize complex proteomes under native conditions and
ultimately produces a full picture of endogenous protein complexes in cells. It requires
novel analytical platforms for high-resolution and liquid-phase separation of protein
complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size
exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was
developed for native proteomics in discovery mode, resulting in the identification of 144
proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli
proteome. The protein complexes include four protein homodimers, 16 protein-metal
complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half
of them have not been reported in the literature. This work represents the first example
of online liquid-phase separation-MS/MS for characterization of a complex proteome
under the native condition, offering the proteomics community an efficient and simple
platform for native proteomics
Measuring the Thermodynamic Stability of Strong Protein-Protein Interactions in Lipid Bilayers Using a Steric Trap
Measuring the Thermodynamic Stability of Strong Protein-Protein Interactions in Lipid Bilayers Using a Steric Trap
Developing a Universal Steric Trapping Strategy for Studying Folding and Stability of Helical Membrane Proteins
Membrane Depth-Dependent Energetic Contribution of the Tryptophan Side Chain to the Stability of Integral Membrane Proteins
Lipid
solvation provides the primary driving force for the insertion
and folding of integral membrane proteins. Although the structure
of the lipid bilayer is often simplified as a central hydrophobic
core sandwiched between two hydrophilic interfacial regions, the complexity
of the liquid-crystalline bilayer structure and the gradient of water
molecules across the bilayer fine-tune the energetic contributions
of individual amino acid residues to the stability of membrane proteins
at different depths of the bilayer. The tryptophan side chain is particularly
interesting because despite its widely recognized role in anchoring
membrane proteins in lipid bilayers, there is little consensus about
its hydrophobicity among various experimentally determined hydrophobicity
scales. Here we investigated how lipid-facing tryptophan residues
located at different depths in the bilayer contribute to the stability
of integral membrane proteins using outer membrane protein A (OmpA)
as a model. We replaced all lipid-contacting residues of the first
transmembrane β-strand of OmpA with alanines and individually
incorporated tryptophans in these positions along the strand. By measuring
the thermodynamic stability of these proteins, we found that OmpA
is slightly more stable when tryptophans are placed in the center
of the bilayer and that it is somewhat destabilized as tryptophans
approach the interfacial region. However, this trend may be partially
reversed when a moderate concentration of urea rather than water is
taken as the reference state. The measured stability profiles are
driven by similar profiles of the <i>m</i>-value, a parameter
that reflects the shielding of hydrophobic surface area from water.
Our results indicate that knowledge of the free energy level of the
protein’s unfolded reference state is important for quantitatively
assessing the stability of membrane proteins, which may explain differences
in observed profiles between <i>in vivo</i> and <i>in vitro</i> scales
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Membrane Induces Contraction but not Collapse of the Denatured State of a Helical Membrane Protein
Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme
Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH
ATP-dependent protein degradation
mediated by AAA+ proteases is
one of the major cellular pathways for protein quality control and
regulation of functional networks. While a majority of studies of
protein degradation have focused on water-soluble proteins, it is
not well understood how membrane proteins with abnormal conformation
are selectively degraded. The knowledge gap stems from the lack of
an in vitro system in which detailed molecular mechanisms can be studied
as well as difficulties in studying membrane protein folding in lipid
bilayers. To quantitatively define the folding-degradation relationship
of membrane proteins, we reconstituted the degradation using the conserved
membrane-integrated AAA+ protease FtsH as a model degradation machine
and the stable helical-bundle membrane protein GlpG as a model substrate
in the lipid bilayer environment. We demonstrate that FtsH possesses
a substantial ability to actively unfold GlpG, and the degradation
significantly depends on the stability and hydrophobicity near the
degradation marker. We find that FtsH hydrolyzes 380–550 ATP
molecules to degrade one copy of GlpG. Remarkably, FtsH overcomes
the dual-energetic burden of substrate unfolding and membrane dislocation
with the ATP cost comparable to that for water-soluble substrates
by robust ClpAP/XP proteases. The physical principles elucidated in
this study provide general insights into membrane protein degradation
mediated by ATP-dependent proteolytic systems